Update: I had a new transmission brake drum machined for the underdrive and I had the drum, adapter, and the Tom Woods DC drive-shaft balanced as one completed unit. The parts were marked for orientation and put back on the D90. After all of this, I still have a vibration! It was a little better, but I still get distinct vibrations starting around 28MPH. I also removed the middle seatbox cover and t-case boot so I could view the drive train while driving on the road. This did not help to isolated the vibrations, the drum and driveshaft seemed to be rotating smoothly. When I felt the t-case and underdrive, there was definitely a difference. The underdrive had more vibration, but this may be because it is hanging off the back of the t-case unsupported while the t-case is supported by the mounts.
Has anyone heard of a Ashcroft underdrive unit causing unwanted vibrations?